Microbial Natural Products and Biosynthesis

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

The paper identifies secondary metabolites in anoxic Cariaco Basin microorganisms using genome mining and gene expression analysis, showing redox potential and lifestyle affect their production.

Automated genome mining predicts combinatorial diversity and taxonomic distribution of peptide metallophore structures

The paper introduces an automated method to identify non-ribosomal peptide metallophore biosynthesis gene clusters in bacterial genomes, revealing widespread occurrence and untapped diversity.

Cost-effective hybrid long-short read assembly delineates alternative GC-rich Streptomyces chassis for natural product discovery

This paper presents a cost-effective hybrid sequencing approach for assembling GC-rich Streptomyces genomes, enabling accurate biosynthetic gene cluster identification and revealing a new species.

Evolution Inspired Engineering of Megasynthetases

The paper describes an evolution-inspired method to engineer NRPS by identifying a recombination breakpoint and using it to assemble NRPS fragments for producing a proteasome inhibitor.

Metabolomic comparison using Streptomyces spp. as a factory of secondary metabolites

The paper compares metabolomic profiles of two Streptomyces strains from extreme environments using GNPS to identify unique secondary metabolites.

A draft genome of the ascomycotal fungal species Pseudopithomyces maydicus (family Didymosphaeriaceae)

The paper presents a draft genome of Pseudopithomyces maydicus, identifying gene models and biosynthetic gene clusters.

TaxiBGC: a Taxonomy-guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes

TaxiBGC improves BGC prediction in metagenomes by using taxonomy-guided methods, showing better performance than read-based approaches and linking BGCs to human diseases.

NPOmix: a machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters

NPOmix connects mass spectrometry fragmentation data to biosynthetic gene clusters using a k-nearest neighbor classifier, improving metabolite discovery and structure prediction.

Genome mining as a biotechnological tool for the discovery of novel biosynthetic genes in lichens

This study mines lichen-forming fungal genomes to identify novel biosynthetic genes, finding 43 potentially novel gene clusters encoding structurally and functionally unknown natural products.

A candidate gene cluster for the bioactive natural product gyrophoric acid in lichen-forming fungi

The paper identifies the biosynthetic gene cluster for gyrophoric acid in lichen-forming fungi using long-read sequencing and bioinformatics.

Activating natural product synthesis using CRISPR interference and activation systems in Streptomyces

This paper develops CRISPRi and CRISPRa systems in Streptomyces to activate silent biosynthetic gene clusters for antibiotic discovery.

A systematic investigation of lactic acid bacteria-derived biosynthetic gene clusters reveals diverse antagonistic bacteriocins in the human microbiome

The paper identifies diverse antagonistic bacteriocins from lactic acid bacteria in the human microbiome using metagenomic and metatranscriptomic analysis.

Genome sequence of the aurodox-producing bacterium Streptomyces goldiniensis ATCC 21386

The paper reports the genome sequence of Streptomyces goldiniensis ATCC 21386, which produces the polyketide aurodox, and identifies biosynthetic gene clusters.

Pangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets

The paper analyzes enterobacterial genomes to identify secondary metabolite gene clusters, finding 8604 BGCs across 2627 genomes and associating some with specific biological functions.

In vivo production of pederin by labrenzin pathway expansion

The paper reports the first successful production of pederin by engineering a marine bacterium with a synthetic gene from the pederin biosynthetic cluster.

Resistance-guided mining of bacterial genotoxins defines a family of DNA glycosylases

The paper identifies AlkZ and AlkX DNA glycosylases involved in bacterial resistance to genotoxins, linking them to specific antimicrobial production.

Simple cloning of large natural product biosynthetic gene clusters from Streptomyces by an engineered CRISPR/Cas12a system

The paper develops a method to efficiently clone large GC-rich BGCs from Streptomyces genomes using a CRISPR/Cas12a-based system, demonstrating its effectiveness with a 87-kb BGC.

In silico analyses of maleidride biosynthetic gene clusters

This work identifies ten new maleidride biosynthetic gene clusters through genome mining and phylogenetic analysis of fungal genomes.

Genome-guided discovery of natural products through multiplexed low coverage whole-genome sequencing of soil Actinomycetes on Oxford Nanopore Flongle

The paper uses low-cost, multiplexed Oxford Nanopore Flongle sequencing to assemble Actinomycete genomes and identify biosynthetic gene clusters, linking them to natural products.

Secondary metabolism drives ecological breadth in the Xylariaceae

The paper shows that secondary metabolism gene clusters in Xylariales fungi are linked to broader ecological roles and increased gene diversity.

Deep-BGCpred: A unified deep learning genome-mining framework for biosynthetic gene cluster prediction

Deep-BGCpred improves BGC prediction by reducing false positives using deep learning and customized strategies, achieving state-of-the-art results on benchmarks.

A GenoChemetic strategy for derivatization of the violacein natural product scaffold

The paper demonstrates a method to generate diverse halogenated and derivatized analogues of the natural product violacein using synthetic biology and chemistry.

Depside and depsidone synthesis in lichenized fungi comes into focus through a genome-wide comparison of the olivetoric and physodic acid chemotype of Pseudevernia furfuracea

This study identifies a gene cluster and FAS responsible for depside and depsidone biosynthesis in lichenized fungi through comparative genomics and metatranscriptomics.

BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes

BiG-MAP profiles metabolic gene cluster abundance and expression in microbiomes, identifying clusters associated with oral health and disease.

BioCAT: a novel tool to search biosynthetic gene clusters producing nonribosomal peptides with a known structure

BioCAT is a tool that identifies biosynthetic gene clusters for nonribosomal peptides using structure-based search and improves upon existing methods with position-specific scoring and ensemble modeling.

EVALUATION OF ANTIMICROBIAL AND ANTIPROLIFERATIVE ACTIVITIES OF ACTINOBACTERIA ISOLATED FROM THE SALINE LAGOONS OF NORTHWEST PERU

This paper isolates and evaluates actinobacteria from Peruvian saline lagoons, identifying strains with antimicrobial and antiproliferative activities against cancer and bacterial cell lines.

Compendium of secondary metabolite biosynthetic diversity encoded in bacterial genomes

The paper analyzes bacterial genomes and metagenome assembled genomes to assess the diversity of secondary metabolite biosynthesis, finding that only 3% of potential natural products are experimentally characterized.

Engineering site-selective incorporation of fluorine into natural product analogs

This paper describes engineering a fluorine-selective enzyme to produce fluorinated polyketide analogs using E. coli.

A BioBricks toolbox for multiplexed metabolic engineering of central carbon metabolism in the tetracenomycin pathway

The paper develops a BioBricks genetic toolbox for metabolic engineering of the tetracenomycin pathway in Streptomyces coelicolor M1146 to produce analogs.

LmbU directly regulates SLINC_RS02575, SLINC_RS05540 and SLINC_RS42780, which are located outside the lmb cluster and inhibit lincomycin biosynthesis in Streptomyces lincolnensis

This paper identifies three genes regulated by LmbU outside the lmb cluster that inhibit lincomycin biosynthesis in Streptomyces lincolnensis.